We develop ultrafast and single-molecule vibrational spectroscopies to study the molecular dynamics of water, electrochemical interfaces, and diffusion-controlled reactions in solution.
Despite its outsized role in our lives, numerous aspects of water chemistry are poorly understood at a molecular level, largely because of the lack of insightful experimental tools. Water's properties emerge from a complex interplay of interactions at a molecular level, including hydrogen bonding, electrostatics, and repulsion. We study water's hydrogen-bonding network, which fluctuates and rearranges on femtosecond-to-picosecond timescales, and its dynamic interactions with solutes ranging from ions to small molecules to polymers and proteins. These studies address problems such as the phase behavior of thermoresponsive polymers in water and, through the subgroup of Nicholas Lewis, the structure and dynamics of water and ions at charged electrochemical interfaces.
Our group also investigates diffusion-controlled bimolecular reactions, in which two molecules encounter one another, interact nonspecifically, and then recognize and bind through site-specific contacts. Our studies focus on the mechanistic details of this encounter-to-reaction process, historically through protein–protein interactions and DNA hybridization, and increasingly through model small-molecule binding systems studied with single-molecule fluorescence techniques.
In seeking solutions to these problems, our experimental approach is to develop and use structure-sensitive ultrafast vibrational spectroscopy to follow the time evolution of molecular structure. One key technique is two-dimensional infrared spectroscopy, which captures molecular structure and dynamics from femtosecond to kilosecond timescales. We have also introduced fluorescence-encoded infrared (FEIR) spectroscopy, which extends structural vibrational spectroscopy to single molecules, enabling us to study stochastic bimolecular processes one molecule at a time.
More details on all these topics are available on the Tokmakoff Group Website.
California State University Sacramento
B.S.
1989
Stanford University
M.S.
1992
Stanford University
Ph.D.
1995
Technical University of Munich
Alexander von Humboldt Postdoctoral Fellow
1995
University of Chicago
NSF Postdoctoral Fellow
1997
University of California Berkeley
NSF Postdoctoral Fellow
1998
Massachusetts Institute of Technology
Professor
2012
University of Chicago
Professor
Present
University of Chicago
Chair
2021
Andrei Tokmakoff, Time-Dependent Quantum Mechanics and Spectroscopy, 2025 Ed., (University of Chicago, 2025), https://doi.org/10.6082/uchicago.16831.
“Isolating Solvent-Solute Hydrogen Bonding Interactions via 2D IR Solvation Shell Spectroscopy,” Samuel Knight, Nicholas H. C. Lewis, Ian Bongalonta, John Hack, Yumin Lee, and Andrei Tokmakoff, Journal of Chemical Physics, 164 (2026) 124505-1-21. https://doi.org/10.1063/5.0316253.
“Unraveling diffusion-controlled bimolecular reactions using fluorescence correlation spectroscopy.” Seung Yeon Lee, Chih-Tsun Yang, Andrei Tokmakoff, J. Chem. Phys. 165 (2026) 074202. https://doi.org/10.1063/5.0343928.
“Fluorescence-Encoded Infrared Vibrational Spectroscopy with Single-Molecule Sensitivity,” Lukas Whaley-Mayda, Abhirup Guha, Samuel Penwell, and Andrei Tokmakoff, Journal of the American Chemical Society, 143 (2021) 3060–3064. https://dx.doi.org/10.1021/jacs.1c00542.
“Kinetics and dynamics of oligonucleotide hybridization,” Brennan Ashwood and Andrei Tokmakoff, Nature Reviews Chemistry 9 (2025) 305–327. https://doi.org/10.1038/s41570-025-00704-8.
“Splitting of Energetic and Dynamic Base Pairing Cooperativity in DNA Duplexes by an Abasic Site,” Brennan Ashwood†, Michael S. Jones†, Andrew L. Ferguson, and Andrei Tokmakoff, Proceedings of the National Academy of Sciences USA, 120 (2023) e2219124120. https://doi.org/10.1073/pnas.2219124120.
“Correlating picosecond electron transfer and confined water dynamics in Prussian Blue using electrochemical 2D IR spectroscopy,” Nicholas H. C. Lewis, Anuj Pennathur, and Andrei Tokmakoff, PNAS, 123 (2026) e2600644123. https://doi.org/10.1073/pnas.2600644123.
“Development and Characterization of Electrodes for Surface-Specific Attenuated Total Reflection Two-Dimensional Infrared Spectroelectrochemistry,” Melissa Bodine, Vepa Rozyyev, Jeffrey W. Elam, Andrei Tokmakoff, and Nicholas H. C. Lewis, Journal of Physical Chemistry C, 127 (2023) 23199–23211. https://doi.org/10.1021/acs.jpcc.3c05445.
“Exchange-Mediated Transport in Battery Electrolytes: Ultrafast or Ultraslow?” Bogdan Dereka, Nicholas H. C. Lewis, Yong Zhang, Nathan Hahn, Jonathan H. Keim, Scott A. Snyder, Edward Maginn, Andrei Tokmakoff, Journal of the American Chemical Society, 144 (2022) 8591–8604. https://doi.org/10.1021/jacs.2c00154.
“From Networked to Isolated: Observing Water Hydrogen Bonds in Concentrated Electrolytes with Two-Dimensional Infrared Spectroscopy,” Nicholas H. C. Lewis, Bogdan Dereka, Yong Zhang, Edward J. Maginn, and Andrei Tokmakoff, Journal of Physical Chemistry B 126 (2022) 5305–5319. https://doi.org/10.1021/acs.jpcb.2c03341 Data: https://doi.org/10.5281/zenodo.6646898.
“Crossover from Hydrogen to Chemical Bonding,” Bogdan Dereka, Qi Yu, Nicholas H. C. Lewis, William B. Carpenter, Joel M. Bowman, Andrei Tokmakoff, Science, 371 (2021) 160-164. https://doi.org/10.1126/science.abe1951.
“Structural characterization of protonated water clusters confined in HZSM-5 zeolites,” John H. Hack†, James P. Dombrowski†, Xinyou Ma†, Yaxin Chen, Nicholas H. C. Lewis, William B. Carpenter, Chenghan Li, Gregory A. Voth, Harold H. Kung and Andrei Tokmakoff, Journal of the American Chemical Society, 143 (2021) 10203–10213. https://doi.org/10.1021/jacs.1c03205.
“Temperature-Jump 2D IR Spectroscopy with Intensity-Modulated CW Optical Heating,” Brennan Ashwood, Nicholas H. C. Lewis, Paul J. Sanstead, Andrei Tokmakoff, Journal of Physical Chemistry B, 124 (2020) 8665–8677. https://doi.org/10.1021/acs.jpcb.0c07177.
Member, National Academy of Sciences
2022
Fellow, American Academy of Arts and Sciences
2018
Ahmed Zewail Award in Ultrafast Science and Technology, American Chemical Society
2016
Ellis R. Lippincott Award, Optical Society of America
2014
Ernest Plyler Prize, American Physical Society
2012
Fellow, Optical Society of America
2009
National Fresenius Award
2002
Alfred P. Sloan Fellowship
2002
Coblentz Award
2002
David and Lucile Packard Fellowship
2000
Andrei Tokmakoff Elected to National Academy of Sciences, May 3, 2022
Three JFI Faculty elected to American Academy of Arts and Sciences, April 18, 2018